On Contributing to the Progress of Medical Informatics as Publisher.

May 1st, 2017, will mark Dieter Bergemann's 80th birthday. As Chief Executive Officer and Owner of Schattauer Publishers from 1983 to 2016, the biomedical and health informatics community owes him a great debt of gratitude. The past and present editors of Methods of Information in Medicine, the IMIA Yearbook of Medical Informatics, and Applied Clinical Informatics want to honour and thank Dieter Bergemann by providing a brief biography that emphasizes his contributions, by reviewing his critical role as an exceptionally supportive publisher for Schattauer's three biomedical and health informatics periodicals, and by sharing some personal anecdotes. Over the past 40 years, Dieter Bergemann has been an influential, if behind-the-scenes, driving force in biomedical and health informatics publications, helping to ensure success in the dissemination of our field's research and practice.

Triangulation applied to Jan H. van Bemmel.

OBJECTIVE: To describe the person of Jan H. van Bemmel from different points of view. METHOD: Triangulation. RESULTS AND CONCLUSIONS: Jan H. van Bemmel successfully contributed to research and education in medical informatics. He inspired a lot of people in The Netherlands and internationally.

On exemplary scientific conduct regarding submission of manuscripts to biomedical informatics journals.

As the Editors of leading international biomedical informatics journals, the authors report on a recent pattern of improper manuscript submissions to journals in our field. As a guide for future authors, we describe ethical and pragmatic issues related to submitting work for peer-reviewed journal publication. We propose a coordinated approach to the problem that our respective journals will follow. This Editorial is being jointly published in the following journals represented by the authors: Computer Methods and Programs in Biomedicine, International Journal of Medical Informatics, Journal of Biomedical Informatics, Journal of the American Medical Informatics Association, and Methods of Information in Medicine.

The Renewed Promise of Medical Informatics.

The promise of the field of Medical Informatics has been great and its impact has been significant. In 1999, the Yearbook editors of the International Medical Informatics Association (IMIA) - also the authors of the present paper - sought to assess this impact by selecting a number of seminal papers in the field, and asking experts to comment on these articles. In particular, it was requested whether and how the expectations, represented by these papers, had been fulfilled since their publication several decades earlier. Each expert was also invited to comment on what might be expected in the future. In the present paper, these areas are briefly reviewed again. Where did these early papers have an impact and where were they not as successful as originally expected? It should be noted that the extraordinary developments in computer technology observed in the last two decades could not have been foreseen by these early researchers. In closing, some of the possibilities and limitations of research in medical informatics are outlined in the context of a framework that considers six levels of computer applications in medicine and health care. For each level, some predictions are made for the future, concluded with thoughts on fruitful areas for ongoing research in the field.

Design and implementation of a national clinical trials registry.

The authors have developed a Web-based system that provides summary information about clinical trials being conducted throughout the United States. The first version of the system, publicly available in February 2000, contains more than 4,000 records representing primarily trials sponsored by the National Institutes of Health. The impetus for this system has come from the Food and Drug Administration (FDA) Modernization Act of 1997, which mandated a registry of both federally and privately funded clinical trials "of experimental treatments for serious or life-threatening diseases or conditions." The system design and implementation have been guided by several principles. First, all stages of system development were guided by the needs of the primary intended audience, patients and other members of the public. Second, broad agreement on a common set of data elements was obtained. Third, the system was designed in a modular and extensible way, and search methods that take extensive advantage of the National Library of Medicine's Unified Medical Language System (UMLS) were developed. Finally, since this will be a long-term effort involving many individuals and organizations, the project is being implemented in several phases.

Evaluating the coverage of controlled health data terminologies: report on the results of the NLM/AHCPR large scale vocabulary test.

OBJECTIVE: To determine the extent to which a combination of existing machine-readable health terminologies cover the concepts and terms needed for a comprehensive controlled vocabulary for health information systems by carrying out a distributed national experiment using the Internet and the UMLS Knowledge Sources, lexical programs, and server. METHODS: Using a specially designed Web-based interface to the UMLS Knowledge Source Server, participants searched the more than 30 vocabularies in the 1996 UMLS Metathesaurus and three planned additions to determine if concepts for which they desired controlled terminology were present or absent. For each term submitted, the interface presented a candidate exact match or a set of potential approximate matches from which the participant selected the most closely related concept. The interface captured a profile of the terms submitted by the participant and for each term searched, information about the concept (if any) selected by the participant. The term information was loaded into a database at NLM for review and analysis and was also available to be downloaded by the participant. A team of subject experts reviewed records to identify matches missed by participants and to correct any obvious errors in relationships. The editors of SNOMED International and the Read Codes were given a random sample of reviewed terms for which exact meaning matches were not found to identify exact matches that were missed or any valid combinations of concepts that were synonymous to input terms. The 1997 UMLS Metathesaurus was used in the semantic type and vocabulary source analysis because it included most of the three planned additions. RESULTS: Sixty-three participants submitted a total of 41,127 terms, which represented 32,679 normalized strings. More than 80% of the terms submitted were wanted for parts of the patient record related to the patient's condition. Following review, 58% of all submitted terms had exact meaning matches in the controlled vocabularies in the test, 41% had related concepts, and 1% were not found. Of the 28% of the terms which were narrower in meaning than a concept in the controlled vocabularies, 86% shared lexical items with the broader concept, but had additional modification. The percentage of exact meanings matches varied by specialty from 45% to 71%. Twenty-nine different vocabularies contained meanings for some of the 23,837 terms (a maximum of 12,707 discrete concepts) with exact meaning matches. Based on preliminary data and analysis, individual vocabularies contained < 1% to 63% of the terms and < 1% to 54% of the concepts. Only SNOMED International and the Read Codes had more than 60% of the terms and more than 50% of the concepts. CONCLUSIONS: The combination of existing controlled vocabularies included in the test represents the meanings of the majority of the terminology needed to record patient conditions, providing substantially more exact matches than any individual vocabulary in the set. From a technical and organizational perspective, the test was successful and should serve as a useful model, both for distributed input to the enhancement of controlled vocabularies and for other kinds of collaborative informatics research.

Planned NLM/AHCPR large-scale vocabulary test: using UMLS technology to determine the extent to which controlled vocabularies cover terminology needed for health care and public health.

The National Library of Medicine (NLM) and the Agency for Health Care Policy and Research (AHCPR) are sponsoring a test to determine the extent to which a combination of existing health-related terminologies covers vocabulary needed in health information systems. The test vocabularies are the 30 that are fully or partially represented in the 1996 edition of the Unified Medical Language System (UMLS) Metathesaurus, plus three planned additions: the portions of SNOMED International not in the 1996 Metathesaurus Read Clinical Classification, and the Logical Observations Identifiers, Names, and Codes (LOINC) system. These vocabularies are available to testers through a special interface to the Internet-based UMLS Knowledge Source Server. The test will determine the ability of the test vocabularies to serve as a source of controlled vocabulary for health data systems and applications. It should provide the basis for realistic resource estimates for developing and maintaining a comprehensive "standard" health vocabulary that is based on existing terminologies.

The nature of lexical knowledge.

This paper considers the nature of lexical knowledge and its role in language and information processing. The lexicon is the central component of language and plays a pivotal role in current linguistic theory [3, 4] and, increasingly, in natural language processing systems [5-7]. The lexicon embodies information about the lexical items of the language and serves as the foundation for morphologic, syntactic, and semantic processing. The differences as well as commonalities among dictionaries, thesauri, and lexicons are discussed, and distinctions between words, lexical items, and terms are drawn. Next, the scope and content of the SPECIALIST lexicon are presented, followed by a discussion of certain writing conventions that can be troublesome for text processing applications. One approach to handling orthographic and other lexical variation is discussed in a section that reports on the design and implementation of the SPECIALIST lexical programs. The paper concludes with a discussion of controlled terminologies for the medical domain. Throughout the discussion, examples are drawn from the SPECIALIST lexicon and from the other UMLS knowledge sources [8, 9].

The representation of meaning in the UMLS.

The UMLS knowledge sources provide detailed information about biomedical naming systems and databases. The Metathesaurus contains biomedical terminology from an increasing number of biomedical thesauri, and the Semantic Network provides a structure that encompasses and unifies the thesauri that are included in the Metathesaurus. This paper addresses some fundamental principles underlying the design and development of the Metathesaurus and Semantic Network. It begins with a description of the formal properties of thesauri, including the Metathesaurus, and the formal properties of the Semantic Network. It continues with consideration of the principle of semantic locality and how this is reflected in the UMLS knowledge sources. The paper concludes with a discussion of the issues involved in attempting to re-use knowledge and the potential for re-use of the UMLS knowledge sources.

From phenotype to genotype: issues in navigating the available information resources.

OBJECTIVES: As part of an investigation of connecting health professionals and the lay public to both disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases. METHODS: We focused on a set of single gene diseases selected from main topics in MEDLINEplus, the NLM's principal resource focused on consumers. We used publicly available websites to investigate specific questions about the genes and gene products associated with the diseases. We also investigated questions of knowledge and data representation for the information resources and navigational issues. RESULTS: Many online resources are available but they are complex and technical. The major challenges encountered when navigating from phenotype to genotype were (1) complexity of the data, (2) dynamic nature of the data, (3) diversity of foci and number of information resources, and (4) lack of use of standard data and knowledge representation methods. CONCLUSIONS: Three major informatics issues arise from the navigational challenges. First, the official gene names are insufficient for navigation of these web resources. Second, navigational inconsistencies arise from difficulties in determining the number and function of alternate forms of the gene or gene product and maintaining currency with this information. Third, synonymy and polysemy cause much confusion. These are severe obstacles to computational navigation from phenotype to genotype, especially for individuals who are novices in the underlying science. Tools and standards to facilitate this navigation are sorely needed.

The Unified Medical Language System.

In 1986, the National Library of Medicine began a long-term research and development project to build the Unified Medical Language System (UMLS). The purpose of the UMLS is to improve the ability of computer programs to "understand" the biomedical meaning in user inquiries and to use this understanding to retrieve and integrate relevant machine-readable information for users. Underlying the UMLS effort is the assumption that timely access to accurate and up-to-date information will improve decision making and ultimately the quality of patient care and research. The development of the UMLS is a distributed national experiment with a strong element of international collaboration. The general strategy is to develop UMLS components through a series of successive approximations of the capabilities ultimately desired. Three experimental Knowledge Sources, the Metathesaurus, the Semantic Network, and the Information Sources Map have been developed and are distributed annually to interested researchers, many of whom have tested and evaluated them in a range of applications. The UMLS project and current developments in high-speed, high-capacity international networks are converging in ways that have great potential for enhancing access to biomedical information.

Digital library research and application.

The last decade has seen an exponential rise in the amount and the nature of information that is available on the Internet. Internet and World Wide Web technology have raised many technical as well as social and economic issues. The paper begins with a description of the recent digital library research initiative funded by the U.S. federal government. Digital library research addresses a host of informatics issues relevant to the current Internet-based environment. The paper continues with a discussion of some problems in information access, including a discussion of the potential of the Unified Medical Language System for navigating among multiple biomedical information systems. Next, some issues in creating Web-accessible resources for health care consumers are addressed, with a focus on recent work at the National Library of Medicine, including a description of the MEDLINEplus system. The paper ends with a brief discussion of some implications of digital library research for the health informatics community.

From French vocabulary to the Unified Medical Language System: a preliminary study.

The Unified Medical Language System (UMLS) is an extensive source of biomedical knowledge developed and maintained by the U.S. National Library of Medicine (NLM). The UMLS began to include biomedical terms in other languages a few years ago. However, providing foreign terms for existing concepts is only the first step for the UMLS to become international. The current limits of the use of the UMLS in French are analyzed (partial translation, unique source of the translated concepts, improper character set, and absence of lexical resources for lexical matching tools). Some suggestions are given for French to be better integrated into the UMLS, especially for adapting the lexical resources to French. Once completed, our present work is expected to give the UMLS the capability to be effectively queried in French.

Aggregating UMLS semantic types for reducing conceptual complexity.

The conceptual complexity of a domain can make it difficult for users of information systems to comprehend and interact with the knowledge embedded in those systems. The Unified Medical Language System (UMLS) currently integrates over 730,000 biomedical concepts from more than fifty biomedical vocabularies. The UMLS semantic network reduces the complexity of this construct by grouping concepts according to the semantic types that have been assigned to them. For certain purposes, however, an even smaller and coarser-grained set of semantic type groupings may be desirable. In this paper, we discuss our approach to creating such a set. We present six basic principles, and then apply those principles in aggregating the existing 134 semantic types into a set of 15 groupings. We present some of the difficulties we encountered and the consequences of the decisions we have made. We discuss some possible uses of the semantic groups, and we conclude with implications for future work.

Methods in year 50: preserving the past and preparing for the future.

BACKGROUND: Founded in 1962 and, therefore, the oldest international journal in medical informatics, Methods of Information in Medicine will publish its 50th volume in 2011. At the start of the journal's sixth decade, a discussion on the journal's profile seems appropriate. OBJECTIVES: To report on the new opportunities for online access to Methods publications as well as on the recent strategic decisions regarding the journal's aims and editorial policies. METHODS: Describing and analyzing the journal's aims and scope. Reflecting on recent publications and on the journal's development during the last decade. RESULTS: From 2011 forward all articles of Methods from 1962 until the present can be accessed online. Methods of Information in Medicine stresses the basic methodology and scientific fundamentals of processing data, information and knowledge in medicine and health care. Although the journal's major focus is on publications in medical informatics, it has never been restricted to publications only in this discipline. For example, articles in medical biometry, in or close to biomedical engineering, and, later, articles in bioinformatics continue to be a part of this journal. CONCLUSIONS: There is a continuous and, as it seems, ever growing overlap in the research methodology and application areas of the mentioned disciplines. As there is a continuing and even growing need for such a publication forum, Methods of Information in Medicine will keep its broad scope. As an organizational consequence, the journal's number of associate editors has increased accordingly.

Data analysis and data mining: current issues in biomedical informatics.

BACKGROUND: Medicine and biomedical sciences have become data-intensive fields, which, at the same time, enable the application of data-driven approaches and require sophisticated data analysis and data mining methods. Biomedical informatics provides a proper interdisciplinary context to integrate data and knowledge when processing available information, with the aim of giving effective decision-making support in clinics and translational research. OBJECTIVES: To reflect on different perspectives related to the role of data analysis and data mining in biomedical informatics. METHODS: On the occasion of the 50th year of Methods of Information in Medicine a symposium was organized, which reflected on opportunities, challenges and priorities of organizing, representing and analysing data, information and knowledge in biomedicine and health care. The contributions of experts with a variety of backgrounds in the area of biomedical data analysis have been collected as one outcome of this symposium, in order to provide a broad, though coherent, overview of some of the most interesting aspects of the field. RESULTS: The paper presents sections on data accumulation and data-driven approaches in medical informatics, data and knowledge integration, statistical issues for the evaluation of data mining models, translational bioinformatics and bioinformatics aspects of genetic epidemiology. CONCLUSIONS: Biomedical informatics represents a natural framework to properly and effectively apply data analysis and data mining methods in a decision-making context. In the future, it will be necessary to preserve the inclusive nature of the field and to foster an increasing sharing of data and methods between researchers.

The birth and evolution of a discipline devoted to information in biomedicine and health care. As reflected in its longest running journal.

BACKGROUND: The journal Methods of Information in Medicine, founded in 1962, has now completed its 50th volume. Its publications during the last five decades reflect the formation of a discipline that deals with information in biomedicine and health care. OBJECTIVES: To report about 1) the journal's origin, 2) the individuals who have significantly contributed to it, 3) trends in the journal's aims and scope, 4) influential papers and 5) major topics published in Methods over the years. METHODS: Methods included analysing the correspondence and journal issues in the archives of the editorial office and of the publisher, citation analysis using the ISI and Scopus databases, and analysing the articles' Medical Subject Headings (MeSH) in MEDLINE. RESULTS: In the journal's first 50 years 208 editorial board members and/or editors contributed to the journal's development, with most individuals coming from Europe and North America. The median time of service was 11 years. At the time of analysis 2,456 articles had been indexed with MeSH. Topics included computerized systems of various types, informatics methodologies, and topics related to a specific medical domain. Some MeSH topic entries were heavily and regularly represented in each of the journal's five decades (e.g. information systems and medical records), while others were important in a particular decade, but not in other decades (e.g. punched-card systems and systems integration). Seven papers were cited more than 100 times and these also covered a broad range of themes such as knowledge representation, analysis of biomedical data and knowledge, clinical decision support and electronic patient records. CONCLUSIONS: Methods of Information in Medicine is the oldest international journal in biomedical informatics. The journal's development over the last 50 years correlates with the formation of this new discipline. It has and continues to stress the basic methodology and scientific fundamentals of organizing, representing and analysing data, information and knowledge in biomedicine and health care. It has and continues to stimulate multidisciplinary communication on research that is devoted to high-quality, efficient health care, to quality of life and to the progress of biomedicine and the health sciences.